Crystal Structure of Staphylococcus Aureus Clumping Factor A in Complex with Fibrinogen Derived Peptide and Uses Thereof

ABSTRACT

The present invention discloses crystal structure of  Staphylococcus aureus  Clumping factor A (ClfA) in complex with fibrinogen (Fg) derived peptide. Also, the present invention also discloses the use of this structure in the design of ClfA targeted vaccines and therapeutic agents (including monoclonal antibodies). In addition, the present invention discloses isolated and purified engineered  Staphylococcus  clumping factor A protein (ClfA) with a stabilized, closed conformation and immunogenic compositions thereof including methods of treating a  Staphylococcus  infection in an individual.

CROSS-REFERENCE TO RELATED APPLICATIONS

This patent application is a continuation of U.S. application Ser. No.14/618,738, filed Feb. 10, 2015, which is a continuation of U.S.application Ser. No. 13/605,567 filed Sep. 6, 2015, which is adivisional patent application of U.S. application Ser. No. 12/459,327,filed Jun. 30, 2009, now U.S. Pat. No. 8,280,643, which claims priorityto U.S. Provisional Application Ser. No. 61/133,537, filed Jun. 30,2008, the contents of which are incorporated by reference herein intheir entirety.

STATEMENT OF FEDERALLY FUNDED RESEARCH

This invention was made with government support under Grant no. AI20624awarded by the National Institutes of Health. The government has certainrights in the invention.

REFERENCE TO A SEQUENCE LISTING

The present application includes a Sequence Listing filed separately asrequired by 37 CFR 1.821-1.825.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention relates generally to the fields of proteinchemistry, immunology, therapeutic pharmaceuticals, and vaccinedevelopment. More specifically, the present invention discloses crystalstructure of Staphylococcus aureus clumping factor A (ClfA) in complexwith fibrinogen (Fg) derived peptide and its use in the design of ClfAtargeted vaccines and therapeutic agents (including monoclonalantibodies).

2. Description of the Related Art

Staphylococcus aureus is a Gram-positive commensal organism thatpermanently colonizes 20% of healthy adults and transiently colonizes upto 50% of the population (1). For many years, S. aureus has been a majornosocomial pathogen causing a range of diseases from superficial skininfections to life-threatening conditions, including septicemia,endocarditis and pneumonia (1-2). Within the last decade an increasingnumber of invasive infections caused by community-acquired S. aureushave been recorded in otherwise healthy children and young adults (3-4).The continued emergence of antibiotic resistance among clinical strainshas made the treatment of staphylococcal infections challenging,underscoring the need for new prevention and treatment strategies (1).

A detailed characterization of the molecular pathogenesis of S. aureusinfections may expose new targets for the development of novel vaccinesand therapeutics. Several staphylococcal virulence factors have beenidentified including capsule, surface adhesins, proteases, and toxins(5-8). One of these virulence factors is the MSCRAMM clumping factor A(ClfA). ClfA is the major staphylococcal fibrinogen (Fg) binding proteinand is responsible for S. aureus clumping in blood plasma (9-10).Essentially all S. aureus clinical strains carry the clfA gene (11);ClfA is a virulence factor in a mouse model of septic arthritis (12) andin rabbit and rat models of infective endocarditis (13-15).

ClfA generates strong immune responses and has shown potential as avaccine component in active and passive immunization studies. In onestudy, mice vaccinated with a recombinant ClfA segment containing theFg-binding domain and subsequently infected with S. aureus showedsignificantly lower levels of arthritis (12). In another study, micepassively immunized with polyclonal or monoclonal antibodies against theClfA Fg-binding domain were protected in a model of septic death (16).The humanized monoclonal antibody, Aurexis® has a high affinity for ClfAand inhibits ClfA binding to Fg (17). Aurexis is currently in clinicaltrials in combination with antibiotic therapy for the treatment of S.aureus bacteremia (18).

ClfA belongs to a class of cell wall-localized proteins that arecovalently anchored to the peptidoglycan (6, 19-20). Starting from theN-terminus, ClfA contains a signal sequence followed by theligand-binding A region composed of three domains (N1, N2, and N3), theserine-aspartate repeat domain (R region), and C-terminal featuresrequired for cell wall anchoring such as the LPXTG motif, atransmembrane segment and a short cytoplasmic domain (21-23). A crystalstructure of a Fg-binding ClfA segment (residues 221-559) which includestwo of the domains (N2N3) demonstrates that each domain adopts anIgG-like fold (24). This domain architecture was also determined fromthe crystal structure of the ligand binding segment of theStaphylococcus epidermidis SdrG, an MSCRAMM that binds to the N-terminalregion of the Fg β-chain (25).

Molecular modeling and sequence analysis indicated that thestaphylococcal Fg binding MSCRAMMs ClfB and FnbpA could also have astructural organization similar to that of SdrG and ClfA, setting thestage for a common mechanism of ligand binding. For SdrG, a dynamicmechanism of Fg binding termed “Dock, Lock and Latch” (DLL) has beenproposed based on a comparison of the crystal structures of SdrG N2N3 asan apo-protein and in complex with a synthetic peptide mimicking thetargeted site in Fg (25). In the SdrG DLL model, the apo-form of theprotein adopts an open conformation that allows the Fg ligand access toa binding trench between the N2 and N3 domains. As the ligand peptidedocks into the trench, a flexible C-terminal extension of the N3 domainis redirected to cover the ligand peptide and “lock” it in place.Subsequently the C-terminal part of this extension interacts with the N2domain and forms a β-strand complementing a β-sheet in the N2 domain.This inserted β-strand serves as a latch to form a stable MSCRAMM ligandcomplex.

ClfA binds to the C-terminus of the Fg γ-chain (9, 23) and a synthetic17 amino acid peptide corresponding to this region was shown to bind toClfA. Interestingly, the A-region of another staphylocccal MSCRAMM FnbpAprotein and human platelet α_(IIb)β₃ integrin also binds to the sameregion in Fg (23, 26-28). A recombinant form of ClfA has been shown toinhibit platelet aggregation and the binding of platelets to immobilizedFg (9). Although the individual N2 and N3 sub-domains in SdrG and ClfAare structurally similar, the overall orientation of one with respect tothe other is different.

Thus, prior art is deficient in structural characterization of how ClfAbinds Fg and its use in the design of vaccines and therapeutic compoundsfor the prevention and treatment of staphylococcal infections. Thecurrent invention fulfills this long standing need in the art.

SUMMARY OF THE INVENTION

The present invention discloses crystal structure of Staphylococcusaureus clumping factor A (ClfA) in complex with fibrinogen (Fg) derivedpeptide. Further, the present invention also discloses the use of thisstructure and any structural information in the design of ClfA targetedvaccines and therapeutic agents (including monoclonal antibodies).

The present invention is directed to a therapeutic agent that bindsMicrobial Surface Components Recognizing Adhesive Matrix Molecules(MSCRAMM) with higher binding affinity than native fibrinogen (Fg). Arepresentative agent comprises an amino acid sequence that differs fromamino acid sequence of a native fibrinogen in at least one amino acidresidue.

The present invention also is directed to an anti-MSCRAMM:fibrinogenantibody effective to inhibit MSCRAMM:fibrinogen interaction but doesnot affect binding of other proteins to fibrinogen.

The present invention is directed further to a method for determiningmodel structure of MSCRAMM in complex with fibrinogen. Such a methodcomprises determining amino acid residue in the MSCRAMM binding regionof native fibrinogen that is critical for the MSCRAMM:fibrinogeninteraction; determining amino acid residue of the MSCRAMM that binds tosaid MSCRAMM binding region of native fibrinogen; and performingcomputational modeling of the MSCRAMM sequence that binds to the MSCRAMMbinding region of native fibrinogen, thereby determining the structureof the MSCRAMM in complex with the fibrinogen.

The present invention is directed further still to a crystal structureof a Staphylococcus clumping factor A (ClfA) protein:fibrinogen derivedpeptide complex that diffracts x-rays for determining atomic coordinatesof the complex with a resolution of about 1.95 angstroms.

The present invention is directed further still to an engineeredstabilized (closed form) of ClfA that binds fibrinogen with higheraffinity as an efficient vaccine candidate. The present invention isdirected to a related immunogenic composition comprising the ClfAprotein described herein and an immunologically acceptable adjuvant ordiluent. The present invention also is directed to a related a method ofvaccinating an individual against a Staphylococcus infection comprisingadministering an immunologically effective amount of the immunogeniccomposition to the individual.

BRIEF DESCRIPTION OF THE DRAWINGS

The appended drawings have been included herein so that theabove-recited features, advantages and objects of the invention willbecome clear and can be understood in detail. These drawings form a partof the specification. It is to be noted, however, that the appendeddrawings illustrate preferred embodiments of the invention and shouldnot be considered to limit the scope of the invention.

FIGS. 1A-1D demonstrate that ClfA₂₂₉₋₅₄₅ binds to Fg g chain peptides.FIG. 1A shows a panel of Fg γ-chain peptides. The wild-type peptidecorresponds to the 17 C-terminal residues of the Fg g-chain (395-411);the mutated peptides have individual amino acids replaced with Ala (orSer). FIG. 1B shows that Fg γ peptides inhibit ClfA binding toimmobilized GST-Fg γ in solid phase assays. Wells were coated with 1 mgGST-Fg γ peptide. ClfA₂₂₉₋₅₄₅ (100 nM) was pre-incubated with wild-typeFg γ peptide (WT g¹⁻¹⁷) or the P1 (G1A) to P17 (V17A) mutant peptide (50mM) for 1 hr. FIG. 1C shows the binding of ClfA to immobilized GST-Fg γand GST-Fg γ P16 using a solid-phase assay. Increasing concentrations ofrClfA₂₂₉₋₅₄₅ were incubated in microtiter wells containing 1 mg GST(circles), GST-Fg γ (triangles) or GST-Fg g P16 (squares). Bound ClfAwas detected with anti-His monoclonal antibodies as described. FIG. 1Dshows the binding of ClfA₂₂₉₋₅₄₅ to Fg γ and Fg γ P16 peptides insolution using ITC.

FIGS. 2A-2D illustrate Fg and Fg γ P16 peptide truncations binding todifferent forms of ClfA. FIG. 2A shows a panel of Fg γ P16 peptides withN- and C-terminal truncations. FIG. 2B shows N-terminal deletions of Fgγ P16 peptide bind ClfA₂₂₉₋₅₄₅ with decreasing affinities. N- andC-terminal truncated Fg γ P16 peptides were tested for their ability tobind ClfA₂₂₉₋₅₄₅ in solution using ITC. FIG. 2C shows a stable closedconformation ClfA₂₂₉₋₅₄₅ was engineered by introducing a disulfidebridge. The left panel shows a ligand blot of rClfA_(D327C/K541C).Recombinant proteins were run in an SDS-PAGE in the presence or absenceof 5 mM DTT and stained with Coomassie Blue (left panel) or transferredto a PDVF membrane (middle panel). Transferred proteins were probed withFg (10 mg/ml) and detected with anti-Fg and AP-conjugated secondaryantibodies. (Right panel) The purified closed form of ClfA_(327C/541C)used for crystallization and ClfA₂₂₉₋₅₄₅ were run in an SDS-PAGE andstained with Coomassie Blue (right panel). FIG. 2D shows the closedconformation of ClfA_(D327C/K541C) binds immobilized Fg and GST-Fg γP16. ClfA₂₂₉₋₅₄₅ or ClfA_(D327C/K541C) was incubated with wells coatedwith either Fg or GST-Fg γ P16 and detected with anti-His monoclonalantibodies as described below.

FIGS. 3A-3D are a representation of ClfA_(D327C/K541C) (N2-N3)-peptidecomplex. FIG. 3A is the ribbon representation of ClfA-peptide (Fgγ-chain analog) complex. The peptide is shown as ball and stick model.2Fo-Fc map around the peptide contoured at 1.sigma. is shown in theclose-up view. FIG. 3B is a stereo view of the superposition of the twocomplexes (A:C and B:D) in the asymmetric unit. FIG. 3C is a schematicrepresentation of ClfA-Fg γ-peptide main-chain parallelβ-complementation interaction. The anti-parallel β-complementationobserved in SdrG₂₇₃₋₅₉₇-Fg β-peptide complex is also shown forcomparison. The residue numbers of both the Fg γ-chain sequence and thepeptide numbering (1-17), in parenthesis, are shown. FIG. 3D is astereo-view showing the side-chain interactions of the ClfA-Fg γ-peptidecomplex. Carbon atoms of the peptide are shown in grey; oxygen, red;nitrogen, blue. Side chain atoms of ClfA are shown as pink stickobjects. Hydrogen bonds are shown as dotted lines.

FIGS. 4A-4C illustrate the superposition of apo-ClfA, ClfA-peptide andSdrG-peptide structures. FIG. 4A shows the superposition ofapo-ClfA₂₂₁₋₅₅₉, ClfA_(D327C/K541C)-peptide complex. The N3 domains ofthe two structures are superposed showing significant deviation in theinter-domain orientations. Apo-ClfA is shown as a cyan ribbon object andClfA-peptide complex is shown in green. In FIG. 4B only N3 domain ofapo-ClfA (cyan) is shown for clarity. The folded-back residues of theC-terminal residues of the apo-ClfA are shown in red. The Fg γ-chainpeptide is shown as blue ribbon. FIG. 4C shows the superposition ofClfA-peptide and SdrG-peptide complexes. The peptide moleculescorresponding to ClfA and SdrG complexes are shown as red and blueribbon objects respectively. ClfA is colored by secondary structure andSdrG is shown as thin yellow uniform coil.

FIGS. 5A-5C illustrate species specificity of ClfA-Fg binding. FIG. 5Ashows that the closed conformation rClfA_(327C/541C) binds immobilizedFg from different animal species with different apparent affinities in asolid-phase assay. FIG. 5B shows that the ClfA_(D327C/K541C) binds humanFg γ P16 peptide with a higher affinity than bovine Fg γ peptide usingITC. FIG. 5C shows that the sequence comparison of human and bovine Fgγ-chain C-terminal residues (top). CPK representation of the bindingpocket formed between the N2 and N3 domains bound to human versus bovineFg γ peptide. ClfA is shown as grey CPK object and peptide atoms areshown in black (bottom).

FIG. 6 illustrates that the γ¹⁻¹⁷ _(D16A) and γ¹⁻¹⁷ _(K12A) peptidesbind weakly to platelet integrin α_(IIb)β₃. Inhibition of Fg γ peptides(γ¹⁻¹⁷ _(D16A) and γ¹⁻¹⁷ _(K12A) and γ¹⁻¹⁷; WT) on binding of fulllength Fg immobilized onto α_(IIb)β₃. Wild-type Fg-γ¹⁻¹⁷ peptide(square) inhibits Fg binding to α_(IIb)β₃ whereas γ¹⁻¹⁷ _(D16A)(triangle) and γ¹⁻¹⁷ _(K12A) (inverted triangle) peptides have verylittle inhibitory effect.

FIGS. 7A-7B illustrate FnbpA binding to GST-Fg γ chain peptides. FIG. 7Ashows that Fg γ peptides inhibit FnbpA₁₉₄₋₅₁₁ binding to immobilizedGST-Fg γ. Wells were coated with 1 mg GST-Fg γ peptide. FnbpA₁₉₄₋₅₁₁(400 nM) was pre-incubated with wild-type Fg γ peptide (WT γ¹⁻¹⁷) or theP1 (G1A) to P17 (V17A) mutant peptide (50 mM) for 1 hr. FIG. 7B is theribbon representation of FnbpA₁₉₄₋₅₁₁:Fg-γ-chain peptide binding model.N2 and N3 domains in FnbpA are shown as ribbons and peptide is shown asstick object.

DETAILED DESCRIPTION OF THE INVENTION I. Definitions

The use of the word “a” or “an” when used in conjunction with the term“comprising” in the claims and/or the specification may mean “one,” butit is also consistent with the meaning of “one or more,” “at least one,”and “one or more than one.” Some embodiments of the invention mayconsist of or consist essentially of one or more elements, method steps,and/or methods of the invention. It is contemplated that any method orcomposition described herein can be implemented with respect to anyother method or composition described herein.

The use of the term “or” in the claims is used to mean “and/or” unlessexplicitly indicated to refer to alternatives only or the alternativesare mutually exclusive, although the disclosure supports a definitionthat refers to only alternatives and “and/or.”

As used herein, the term “immunologically effective amount” refers to anamount that results in an improvement or remediation of the symptoms ofthe disease or condition due to induction of an immune response. Thoseof skill in the art understand that the effective amount may improve thepatient's or subject's condition, but may not be a complete cure of thedisease and/or condition.

As used herein, “active immunization” is defined as the administrationof a vaccine to stimulate the host immune system to develop immunityagainst a specific pathogen or toxin.

As used herein, “passive immunization” is defined as the administrationof antibodies to a host to provide immunity against a specific pathogenor toxin.

As used herein, “CpG oligonucleotides” are defined by the presence of anunmethylated CG dinucleotide in a CpG motif.

As used herein, “adjuvant” is defined as a substance which when includedin a vaccine formulation non-specifically enhances the immune responseto an antigen.

II. Present Invention

In one embodiment of the present invention there is provided atherapeutic agent that binds Microbial Surface Components RecognizingAdhesive Matrix Molecules (MSCRAMM) with higher binding affinity thannative fibrinogen (Fg), the agent comprising amino acid sequence thatdiffers from amino acid sequence of a native Fibrinogen in at least oneamino acid residue. Examples of such an agent may include but is notlimited to a peptide, a fusion protein, a small molecule inhibitor or asmall molecule drug. Examples of the peptide may include but is notlimited to a P16 peptide (Asp16→Ala), a P12 peptide (Lys12→Ala) orcombination thereof. Further, examples of MSCRAMM may include but is notlimited to a clumping factor A (ClfA), FnbpA, FnbpB or Fbl and theMSCRAMM may include but is not limited to those present on the surfaceof Staphylococcus aureus, Staphylococcus lugdunensis, or Staphylococcusepidermis.

In another embodiment of the present invention there is provided amethod for inhibiting Microbial Surface Components Recognizing AdhesiveMatrix Molecule (MSCRAMM):Fibrinogen (Fg) interaction, comprising:contacting an MSCRAMM with the above-described therapeutic agent,thereby inhibiting the MSCRAMM:Fibrinogen interaction. The therapeuticagent may not affect α_(IIb)β₃ intergrin interaction.

In yet another embodiment of the present invention there is provided apharmaceutical composition, comprising: the above-described therapeuticagent and a pharmaceutically acceptable carrier.

In yet another embodiment of the present invention there is provided amethod of treating and/or preventing bacterial infection caused or dueat least in part to a MSCRAMM:fibrinogen interaction in an individual,comprising: administering pharmacologically effective amounts of thepharmaceutical composition described supra such that administration ofthe composition inhibits binding of MSCRAMM to native fibrinogen anddoes not affect α_(IIb)β₃ intergrin interaction. Examples of thebacteria may include but is not limited to Staphylococcus aureus,Staphylococcus lugdunensis, or Staphylococcus epidermis. Further, theroutes of administration of the pharmaceutical composition may includebut is not limited to subcutaneous, intravenous, intramuscular, intranasal, vaginal, or oral routes. One of ordinary skill in the art isreadily able to determine a suitable dosage. Additionally, theindividual who may benefit from such a method may include but is notlimited to one who is a healthy individual, an individual diagnosed withthe bacterial infection, at risk of developing bacterial infection orsuspected of suffering from the bacterial infection.

In yet another embodiment of the present invention there is provided ananti-MSCRAMM:fibrinogen antibody effective to inhibit anMSCRAMM:fibrinogen interaction but not affecting binding of otherproteins to fibrinogen. Such an antibody may be generated using peptidescomprising MSCRAMM binding region on fibrinogen, the peptide differingfrom the native Fibrinogen in at least one amino acid residue. Examplesof the peptide may include but is not limited to a P16 peptide(Asp16→Ala), a P12 peptide (Lys12→Ala) or combination thereof.Alternatively, the antibody may be generated using peptides derived fromfibrinogen binding region of MSCRAMM, the peptide differing from thenative MSCRAMM in at least one amino acid residue. Further, the antibodymay be a monoclonal antibody, a polyclonal antibody or a chimericantibody. Furthermore, the MSCRAMM may be present on Staphylococcusaureus, Staphylococcus lugdunensis, or Staphylococcus epidermis.

In yet another embodiment of the present invention there is provided amethod of treating a bacterial infection in an individual, comprising:administering immunologically effective amounts of the above-describedanti-MSCRAMM:fibrinogen antibody to the individual, thereby treating thebacterial infection in the individual. Such an antibody may inhibitsinteraction between MSCRAMM and Fibrinogen may not affect the α_(IIb)β₃intergrin interaction. Examples of the individual who may benefit fromthis method may include but is not limited to one who is diagnosed withthe infection, is at risk of developing the infection or is suspected ofsuffering from the infection. One of ordinary skill in the art isreadily able to determine a suitable dosage. Further, examples of theroutes of administration of the antibody may include subcutaneous,intramuscular, intravenous, intranasal, vaginal, oral, or other mucosalroutes.

In yet another embodiment of the present invention there is provided amethod for determining structure of MSCRAMM in complex with fibrinogen,comprising: determining amino acid residue in the MSCRAMM binding regionof native fibrinogen that is critical for the MSCRAMM:fibrinogeninteraction; determining amino acid residue of the MSCRAMM that binds tothe MSCRAMM binding region of native fibrinogen; and performingcomputational modeling of the MSCRAMM sequence that binds to the MSCRAMMbinding region of native fibrinogen, thereby determining the structureof the MSCRAMM in complex with the fibrinogen. This method may furthercomprise identifying potential agents that inhibit MSCRAMM:fibrinogeninteraction without affecting binding of other proteins to fibrinogen.Such a potential agent may include one that comprises amino acidsequence of MSCRAMM binding region on fibrinogen, the amino acidsequence differing from the fibrinogen in at least one amino acidresidue or an amino acid sequence of fibrinogen binding region ofMSCRAMM, the amino acid sequence differing from the MSCRAMM in at leastone amino acid residue.

Additionally, the amino acid residue in the MSCRAMM binding region ofnative fibrinogen may be determined by: synthesizing control peptidesthat comprise the native fibrinogen sequence that binds MSCRAMM;synthesizing substituted peptides that differ from the control peptidein one or more amino acid residues; and comparing binding of MSCRAMM tonative fibrinogen in presence of control peptide or in presence ofsubstituted peptide, where less potent inhibition of MSCRAMM binding tonative fibrinogen in presence of substituted peptide compared to controlpeptide indicates that the amino acid residue(s) that were substitutedare less important for the MSCRAMM:fibrinogen interaction, whereextensive inhibition of MSCRAMM binding to native fibrinogen in presenceof substituted peptide compared to control peptide indicates that theamino acid residue(s) that were substituted are critical for theMSCRAMM:fibrinogen interaction.

Further, the amino acid residue in the MSCRAMM may be determined bycomparing the stability of a native MSCRAMM:fibrinogen complex with thestability of a mutated MSCRAMM:fibrinogen complex, where said fibrinogenin the complex comprises peptide derived from MSCRAMM binding region ofnative fibrinogen. Examples of the MSCRAMM may include but is notlimited to a clumping factor A (ClfA), FnbpA, FnbpB or Fbl. Further, theMSCRAMM may include but is not limited to one that is present on thesurface of Staphylococcus aureus, Staphylococcus lugdunensis, orStaphylococcus epidermis.

In yet another embodiment of the present invention there is provided acrystal structure of a Staphylococcus clumping factor A protein(ClfA):fibrinogen derived peptide complex that diffracts x-rays fordetermining atomic coordinates of the complex with a resolution of about1.95 angstroms. The Staphylococcus may be those species described supra.In the crystal structure the fibrinogen derived peptide may be a P16peptide (Asp16→Ala) or a P12 peptide (Lys12→Ala) having an N-terminaltruncation -2Nt, -4Nt or -6Nt. Particularly, the crystal structure maybe a ClfA/P16-4Nt complex.

In yet another embodiment of the present invention there is provided anisolated and purified engineered Staphylococcus clumping factor Aprotein (ClfA) with a stabilized, closed conformation. For example, theClfA protein may be ClfA_(D327C/K541C) protein.

In a related embodiment there is provided an immunogenic compositioncomprising the ClfA protein described supra and an immunologicallyacceptable adjuvant or diluent. The immunogenic composition may comprisea vaccine.

In another related embodiment there is provided a method of vaccinatingan individual against a Staphylococcus infection comprisingadministering an immunologically effective amount of the immunogeniccomposition described supra to the individual.

The general purpose of the present invention is to provide a detailedstructural characterization of how ClfA binds Fg and subsequently usethis structural information in the design of vaccines and therapeuticcompounds for the prevention and treatment of staphyloccocal infections.Several of the peptides have been shown to have enhanced binding to Fgbut show decreased binding to host proteins that target the same regionof Fg. The two extensively studied linear peptide binding MSCRAMMs SdrGand ClfA use very similar pockets between the N2 and N3 domains forligand binding but show significant differences in mechanism of binding.Based on the results presented here, it is postulated that the mechanismof interaction between ClfA and Fg is a variation of the “Dock, Lock andLatch (DLL)” model of SdrG binding to Fg. In the DLL model of binding,the apo-form of the SdrG is in an open conformation to allow the ligandaccess to the binding cleft. A closed conformation of SdrG is unable tobind Fg. In the ClfA model, it is believed that the peptide may threadinto the cavity formed in a stabilized closed configuration andtherefore the ClfA-Fg binding mechanism could be called “Latch andDock”.

In the case of CNA, a collagen binding MSCRAMM from S. aureus, thecollagen molecule binds to CNA through a “collagen hug” model (29) whichrepresents yet another variant of the DLL binding mechanism. All threeMSCRAMM-ligand structures determined so far, SdrG, CNA and the ClfA havedifferent ligand binding characteristics and mechanisms, although theoverall structures of the ligand binding regions of these MSCRAMMs arevery similar. These observations suggest that an ancestral MSCRAMM hasevolved to accommodate different ligands without greatly altering theoverall organization of the proteins.

Although there are many antibiotics available in the market to treat S.aureus infections, the strategy discussed herein is a novel approachtargeting ClfA on S. aureus. The primary disadvantage of using a smallsegment (peptide) of the interacting protein molecule is non-specificityand undesirable binding and adverse effects. The process of modifiedpeptide by variations in amino acid will be effective and easier toachieve the much desired specificity. These peptides can besignificantly efficient over any small molecule or any other antibiotictreatment. Based on the structure disclosed herein, two peptides, P16(Asp16→Ala) peptide and P12 (Lys12→Ala) peptide are synthesized and canbe used as inhibitors of ClfA. To further enhance the specificitytowards ClfA and decrease undesirable activation of platelets, acombination of two variants such as double mutant analog (P12+P16) willbe synthesized and tested. The present invention contemplates attemptingfurther variations in the sequence to achieve additional affinitytowards ClfA. These peptides are assessed in a mouse model of S. aureusinduced septic death.

Alternate formulations may include the design of small moleculeinhibitors that specifically bind to ClfA and/or tailoring/modifyexisting small molecule drugs. Several small molecule drugs areavailable that mimic the same region of Fg that bind to integrin. Thefeatures/amino acid differences that contribute to the specificity ofthe peptide can be incorporated in the existing anti-platelet drugmolecules to achieve the specificity for ClfA.

Overall, the present invention provides the Fg/ClfA complex structurethat can be (1) used to develop therapeutics that specifically willinhibit ClfA:Fg interaction but will not affect α_(IIb)β₃ integrininteractions; (2) to design ClfA constructs that will be optimal vaccinecandidates and can be used for the generation and screening oftherapeutic monoclonal antibodies; and (3) to model other MSCRAMM Fginteractions with similar substrate specificities such as FnbpA, FnbpBand FbI.

Treatment methods involve treating and/preventing an infection in anindividual with a pharmacologically effective or an immunologicallyeffective amount of a pharmaceutical composition containing therapeuticagents described herein. Such therapeutic agent may comprise a peptide,fusion peptide, small molecule inhibitor, small molecule drug or anantibody. A pharmacologically effective amount is described, generally,as that amount sufficient to detectably and repeatedly inhibitMSCRAMM:fibrinogen interaction so as to prevent, ameliorate, reduce,minimize or limit the extent of a disease or its symptoms. Animmunologically effective amount is described, generally, as that amountsufficient to detectably and repeatedly induce an immune response so asto prevent, ameliorate, reduce, minimize or limit the extent of adisease or its symptoms. More specifically, it is envisioned that thetreatment with the pharmaceutical composition or an immunogeniccomposition enhances antibody response, reduces the level ofinflammatory cytokines and the levels of endotoxins and decreases thebacterial load in the individual to prevent the infection caused by thebacteria.

The pharmacologically or immunologically effective amount of thecomposition or antibody, respectively to be used are those amountseffective to produce beneficial results, particularly with respect topreventing the infection caused by the bacteria, in the recipient animalor patient. Such amounts may be initially determined by reviewing thepublished literature, by conducting in vitro tests or by conductingmetabolic studies in healthy experimental animals. Before use in aclinical setting, it may be beneficial to conduct confirmatory studiesin an animal model, preferably a widely accepted animal model of theparticular disease to be treated. Preferred animal models for use incertain embodiments are rodent models, which are preferred because theyare economical to use and, particularly, because the results gained arewidely accepted as predictive of clinical value.

The pharmaceutical composition disclosed herein and the antibodygenerated thereof may be administered either alone or in combinationwith another drug, a compound, or an antibiotic. Such a drug, compoundor antibiotic may be administered concurrently or sequentially with theimmunogenic composition or antibody disclosed herein. The effect ofco-administration with the pharmaceutical composition or antibody is tolower the dosage of the drug, the compound or the antibiotic normallyrequired that is known to have at least a minimal pharmacological ortherapeutic effect against the disease that is being treated.Concomitantly, toxicity of the drug, the compound or the antibiotic tonormal cells, tissues and organs is reduced without reducing,ameliorating, eliminating or otherwise interfering with any cytotoxic,cytostatic, apoptotic or other killing or inhibitory therapeutic effectof the drug, compound or antibiotic.

The composition described herein and the drug, compound, or antibioticmay be administered independently, either systemically or locally, byany method standard in the art, for example, subcutaneously,intravenously, parenterally, intraperitoneally, intradermally,intramuscularly, topically, enterally, rectally, nasally, buccally,vaginally or by inhalation spray, by drug pump or contained withintransdermal patch or an implant. Dosage formulations of the compositiondescribed herein may comprise conventional non-toxic, physiologically orpharmaceutically acceptable carriers or vehicles suitable for the methodof administration.

The pharmaceutical composition or antibody described herein and thedrug, compound or antibiotic may be administered independently one ormore times to achieve, maintain or improve upon a therapeutic effect. Itis well within the skill of an artisan to determine dosage or whether asuitable dosage of either or both of the immunogenic composition orantibody and the drug, compound or antibiotic comprises a singleadministered dose or multiple administered doses.

As is well known in the art, a specific dose level of such apharmaceutical composition or antibody for any particular patientdepends upon a variety of factors including the activity of the specificcompound employed, the age, body weight, general health, sex, diet, timeof administration, route of administration, rate of excretion, drugcombination, and the severity of the particular disease undergoingtherapy. The person responsible for administration will determine theappropriate dose for the individual subject. Moreover, for humanadministration, preparations should meet sterility, pyrogenicity,general safety and purity standards as required by FDA Office ofBiologics standards.

One of skill in the art realizes that the pharmacologically effectiveamount of the immunogenic composition or the antibody can be the amountthat is required to achieve the desired result: enhance antibodyresponse, reduce the level of inflammatory cytokines and levels ofendotoxins, decrease the bacterial load, etc.

Administration of the pharmaceutical composition of the presentinvention and the antibody to a patient or subject will follow generalprotocols for the administration of therapies used in treatment ofbacterial infections taking into account the toxicity, if any, of thecomponents in the immunogenic composition, the antibody and/or, inembodiments of combination therapy, the toxicity of the antibiotic. Itis expected that the treatment cycles would be repeated as necessary. Italso is contemplated that various standard therapies, as well assurgical intervention, may be applied in combination with the describedtherapy.

As is known to one of skill in the art the pharmaceutical compositiondescribed herein may be administered along with any of the knownpharmacologically acceptable carriers. Additionally the pharmaceuticalcomposition can be administered via any of the known routes ofadministration such as subcutaneous, intranasal or mucosal. Furthermore,the dosage of the composition to be administered can be determined byperforming experiments as is known to one of skill in the art.

The following examples are given for the purpose of illustrating variousembodiments of the invention and are not meant to limit the presentinvention in any fashion. One skilled in the art will appreciate readilythat the present invention is well adapted to carry out the objects andobtain the ends and advantages mentioned, as well as those objects, endsand advantages inherent herein. Changes therein and other uses which areencompassed within the spirit of the invention as defined by the scopeof the claims will occur to those skilled in the art.

Example 1 Bacterial Strains, Plasmids and Culture Conditions

Escherichia coli XL-1 Blue (Stratagene) was used as the host for plasmidcloning and protein expression. Chromosomal DNA from S. aureus strainNewman was used to amplify the ClfA DNA sequence. All E. coli strainscontaining plasmids were grown on LB media with ampicillin (100 μg/ml).

Example 2 Manipulation of DNA

DNA restriction enzymes were used according to the manufacturer'sprotocols (New England Biolabs) and DNA manipulations were performedusing standard procedures (30) (Sambrook and Gething, 1989). Plasmid DNAused for cloning and sequencing was purified using the Qiagen Miniprepkit (Qiagen). DNA was sequenced by the dideoxy chain termination methodwith an ABI 373A DNA Sequencer (Perkin Elmer, Applied BiosystemsDivision). DNA containing the N-terminal ClfA sequences were amplifiedby PCR (Applied Biosystems) using Newman strain chromosomal DNA aspreviously described (31). The synthetic oligonucleotides (IDT) used foramplifying clfA gene products and for cysteine mutations are listed inTable I.

TABLE 1 C1fA229 5′-CCCGGATCCGGCACAGATATTACGAAT-3′ (SEQ ID NO: 1) C1fA5455′-CCCGGTACCTCAAGGAACAACTGGTTTATC-3′ (SEQ ID NO: 2) rClfA3275′-TGCTTTTACATCACATTTAGTATTTAC-3′ (SEQ ID NO: 3) fC1fA3275′-GTAAATACTAAATGTGATGTAAAAGCA-3′ (SEQ ID NO: 4) C1fA5415′-CCCGGTACCTCAAGGAACAACTGGACAATCGATACCGTC-3′ (SEQ ID NO: 5) Peptides:Wild-type Fg γ 395-411 GEGQQHHLGGAKQAGDV (SEQ ID NO: 6) Fg γ395-411 D410A: GEGQQHHLGGAKQAGAV (SEQ ID NO: 28) P16-2Nt 397-411GQQHHLGGAKQAGAV (SEQ ID NO: 7) P16-4Nt 399-411QHHLGGAKQAGAV (SEQ ID NO: 8) P16-6Nt 401-411 HLGGAKQAGAV (SEQ ID NO: 9)P16-8Nt 403-411 GGAKQAGAV (SEQ ID NO: 10) P16-2Ct 395-409GEGQQHHLGGAKQAG (SEQ ID NO: 11) P16-4Ct 395-407GEGQQHHLGGAKQ (SEQ ID NO: 12)

For Disulfide Mutant: Example 3 Construction of Disulphide MutantsStable Form of ClfA

Cysteine mutations were predicted by comparing ClfA₂₂₁₋₅₅₉ toSdrG₍₂₇₃₋₅₉₇₎ disulfide mutant with stable closed conformations (32) andby computer modeling. A model of ClfA in closed conformation was builtbased on the closed conformation of the SdrG-peptide complex (25). TheCβ-Cβ distances were calculated for a few residues at the C-terminal endof the latch and strand E in the N2 domain. Residue pairs with Cβ-Cβdistance less than 3 Å were changed to cysteines to identify residuesthat could form optimum disulfide bond geometry. The D327C/K541C mutantwas found to form a disulfide bond at the end of the latch. The cysteinemutations in ClfA_(D327C/K541C) were generated by overlap PCR (33-34).The forward primer for PCR extension contained a BamHI restriction siteand the reverse primer contained a KpnI restriction site. Themutagenesis primers contained complementary overlapping sequences. Thefinal PCR product was digested with BamHI and KpnI and was ligated intosame site in the expression vector pQE30 (Qiagen). All mutations wereconfirmed by sequencing. The primers used are listed in Table I.

Example 4 Expression and Purification of Recombinant Proteins

E. coli lysates containing recombinant ClfA and GST-Fg γ-chain fusionproteins were purified as previously described (35). PCR products weresubcloned into expression vector pQE-30 (Qiagen) to generate recombinantproteins containing an N-terminal histidine (His) tag as previouslydescribed (9). The recombinant ClfA His-tag fusion proteins werepurified by metal chelation chromatography and anion exchangechromatography as previously described (23). To generate recombinantClfA₂₂₉₋₅₄₅ and ClfA₂₂₁₋₅₅₉ proteins, PCR-amplified fragments weredigested with BamHI and KpnI and cloned into BamHI/KpnI digested PQE-30.The primers used to generate the recombinant constructs are listed inTable I. The reactions contained 50 ng of strain Newman DNA, 100 pmol ofeach forward and reverse primers, 250 nM of each dNTP, 2 units of PfuDNA polymerase (Stratagene) and 5 ml Pfu buffer in a total volume of 50ml. The DNA was amplified at 94° C. for 1 min, 48° C. for 45 sec; 72° C.for 2 min for 30 cycles, followed by 72° C. for 10 min. The PCR productswere analyzed by agarose gel electrophoresis using standard methods (30)and purified as described above.

Example 5 Enzyme-Linked Immunosorbent Assay

The ability of the wild-type ClfA₂₂₉₋₅₄₅ and disulfide ClfA mutants tobind Fg was analyzed by ELISA-type binding assays. Immulon 4HBXMicrotiter plates (Thermo) were coated with human Fg (1 μg/well) in HBS(10 mM HEPES, 100 mM NaCl, 3 mM EDTA, pH 7.4) over-night at 4° C. Thewells were washed with HBS containing 0.05% (w/v) Tween-20 (HBST) andblocked with 5% (w/v) BSA in HBS for 1 h at 25° C. The wells were washed3 times with HBST and recombinant ClfA proteins in HBS were added andthe plates were incubated at 25° C. for 1 h. After incubation, theplates were washed 3 times with HBST. Anti-His antibodies (GEHealthcare) were added (1:3000 in HBS) and the plates were incubated at25° C. for 1 h. The wells were subsequently washed 3 times with HBST andincubated with Goat anti-mouse-AP secondary antibodies (diluted 1:3000in HBS; Bio-Rad) at 25° C. for 1 h. The wells were washed 3 times withHBST and AP-conjugated polyclonal antibodies were detected by additionof p-nitrophenyl phosphate (Sigma) in 1 M diethanolamine (0.5 mM MgCl₂,pH 9.8) and incubated at 25° C. for 30-60 min. The plates were read at405 nm in an ELISA plate reader (Themomax, Molecular Devices). For theinhibition assays, recombinant ClfA₂₂₉₋₅₄₅ was pre-incubated with Fg γpeptides in HBS for 1 h at 37° C. The recombinant protein-peptidesolutions were then added to plates coated with 1 mg/well GST fusionprotein containing the native human Fg γ 395-411 sequence (called GST-Fgγ¹⁻¹⁷) and bound protein was detected as described above. If the peptidebinds ClfA it would inhibit binding of the GST-Fg γ¹⁻¹⁷ to the MSCRAMM.

Example 6 Synthesis of Gamma Chain Peptides

The wild-type and mutated peptides corresponding to the 17 C-terminalresidues of the fibrinogen γ-chain (residues 395-411) and truncatedversions of this peptide (listed in Table I) were synthesized aspreviously described and purified using HPLC (9).

Example 7 Isothermal Titration Calorimetry

The interaction between ClfA proteins and soluble Fg peptides wasanalyzed by Isothermal titration calorimetry (ITC) using a VP-ITCmicrocalorimeter (MicroCal). The cell contained 30 mM ClfA and thesyringe contained 500-600 mM peptide in HBS buffer (10 mM HEPES, 150 mMNaCl, pH 7.4). All samples were degassed for 5 min. The titration wasperformed at 30° C. using a preliminary injection of 5 ml followed by 30injections of 10 ml with an injection speed of 0.5 ml/sec. The stirringspeed was 300 rpm. Data were fitted to a single binding site model andanalyzed using Origin version 5 (MicroCal) software.

Example 8 Crystallization

The ClfA_(D327C/K541C) protein was purified as described andconcentrated to 30 mg/ml. The synthetic γ-chain peptide analogs, P16 andN-terminal truncations of P16 (P16-2Nt, P16-4Nt and P16-6Nt) were mixedwith the protein at 1:20 molar ratio and left for 30 min at 5° C. Thismixture was screened for crystallization conditions. Small needles ofthe ClfA/P16-2Nt, -4Nt and -6Nt were obtained during initial search ofthe crystallization condition, but we could only successfully optimizeClfA/P16-4Nt and ClfA/P16-6Nt. Diffraction quality crystals wereobtained by mixing 2 μl of protein solution with 2 μl of reservoirsolution containing 16-20% PEG 8K, 110 mM succinic acid pH 6.0.

Example 9 X-Ray Data Collection, Structure Solution and Refinement

Crystals of ClfA/P16-4Nt were flash frozen with a stabilizing solutioncontaining 20% glycerol. Diffraction data were measured on Rigaku R-AxisIV⁺⁺ detector. A total of 180 frames were collected at a detectordistance of 120 mm with 1° oscillation. Data were indexed, integratedand scaled using d*terk (47) (Pflugrath, 1999). The crystals diffractedto 1.95 Å and the data statistics were listed in Table 2. Calculation ofthe Matthews coefficient suggested the presence of 2 copies of themolecule in the unit cell of the triclinic cell. The structure wassolved by molecular replacement (MR) with the program PHASER (36) usingindividual N2 and N3 domains of ClfA as search model. Solutions for theN3 domain were obtained for the two copies followed by the solutions ofN2 domains. Data covering 2.5-15 Å were used for the molecularreplacement solution. Electron density maps calculated during theinitial rounds of refinement showed interpretable density for 11 out of13 peptide residues in both the copies of the complex. Modeling buildingof the peptide and rebuilding of a few loop regions were performed usingthe program COOT (37). A few cycles of ARP/WARP (38) were performed toimprove the map and for the building of water model. After a few cyclesof refinement using Refmac5.0 (39), electron density was clear for onlythe backbone atoms for two remaining N-terminal residues of the peptidemolecule D and one residue for peptide C. The final model of ClfAincluded residues 230-299, 303-452, 456-476 and 479-545 in molecule Aand 230-438, 440-476 and 479-542 in molecule B. The structure wasrefined to a final R-factor of 20.9% and R-free of 27.8%. Stereochemicalquality of the model was validated using PROCHECK (40).

TABLE 2 Crystallographic data measurement and refinement data Celldimensions a, b, c (Å) 35.43, 61.84, 81.78 α, β, γ (°) 85.44, 81.84,82.45 Space group P1 Resolution (Å) 1.95-15.0 Reflections total/unique86051/46090 Completeness (%) 93.9 R_(merge) * 0.074 Number of moleculesin the asymmetric unit 2 Rfactor/R_(free) ⁺ 0.211/0.279 Bond rmsdeviation (Å) 0.015 Angle rms deviation (°) 1.64 Average B value (Å)29.9 No of non-hydrogen atoms 5226 Protein 4558 Peptide 141 Water 527Rms deviations from ideal values Bond lengths (Å) 0.22 Bond Angles (°)1.95 PDB ID 2vr3 * R_(merge) = Σ | I_(j) − <I> |/Σ I_(i); where I_(j) isthe measured and <I> is the mean intensity of reflection hkl; ⁺ R_(free)is calculated over 2% of randomly selected reflections not included inthe refinement.

Example 10 Integrin (α_(IIb)β₃) Inhibition Assay

For α_(IIb)β₃ inhibition assay. α_(IIb)β₃ Immulon 4HBX Microtiter96-well plates (Thermo) were coated with α_(IIb)β₃ (0.25 mg/well) in TBS(25 mM Tris, 3 mM KCl, 140 mM NaCl, pH 7.4) over night at 4° C. Thewells were washed with TBS containing 0.05% (w/v) Tween-20 (TBST). Afterblocking with 3% (w/v) BSA dissolved in TBS for 1 h at RT, 10 nM of fulllength Fg was applied in the presence of either WT γ¹⁻¹⁷, γ¹⁻¹⁷ _(D16A)or γ¹⁻¹⁷ _(K12A) peptides and plates were incubated at RT for anotherhour. The bound full length Fg was then detected by goat anti human Fg(1:1000 dilution, Sigma) antibody followed by horseradishperoxidase-conjugated rabbit anti-goat IgG antibody (1:1000 dilution,Cannel). After incubation with 0.4 mg/ml of substrate,o-phenylenediamine dihydrochloride (OPD, Sigma) dissolved inphosphate-citrate buffer, pH 5.0, bound antibodies were determined in anELISA reader at 450 nm. The proteins, antibodies and peptides werediluted in TBST containing 1% (w/v) BSA, 2 mM MgCl₂, 1 mM of CaCl₂ andMnCl₂.

Example 11 Molecular Modeling

All molecular modeling studies were performed using InsightII software(Accrelys Inc). Modeling of FnbpA-peptide complex was performed using“Homology” module available in InsightII using ClfA₂₂₉₋₅₄₅ peptidecomplex as a template. Prior to model building, the amino acid sequenceof ClfA₂₂₉₋₅₄₅ was aligned with FnbpA (GENBANK® ID: CA077272) usingLalign (41). The aligned sequences were manually checked for any gaps inthe core β-sheet forming regions of ClfA. The final model was subjectedto molecular dynamics simulation followed by conjugate gradient energyminimization. Figures were made using RIBBONS (42). The atomiccoordinates and structure factors of the complex structure have beendeposited in Protein Data Bank with accession number 2vr3.

Example 12 Identification of Critical Residues in Fg Required forBinding to ClfA

In previous studies, a segment of ClfA composed of residues 221-559 wasshown to bind to the C-terminal end of the human Fg γ-chain (9). Basedon structural similarities with SdrG, a smaller ClfA construct (229-545)predicted to be composed only of the N2 N3 domains was designed and itwas shown that ClfA₂₂₉₋₅₄₅ retained the Fg-binding activity. To identifyspecific residues in Fg that are important for binding to ClfA₂₂₉₋₅₄₅, apanel of peptides (FIG. 1A; SEQ ID NOS: 13-29) based on the Fg γ-chainsequence 395-411 (referred to as g¹⁻¹⁷) were synthesized in which eachposition was sequentially substituted with an alanine residue (alanines11 and 14 changed to serines). These peptides were tested as inhibitorsin solid-phase binding assays. Peptides g¹⁻¹⁷ _(H6A), g¹⁻¹⁷ _(H7A),g¹⁻¹⁷ _(G10A), g¹⁻¹⁷ _(Q13A), g¹⁻¹⁷ _(A14S) and g¹⁻¹⁷ _(G15A) weresignificantly less potent inhibitors than the native sequence suggestingthat the Fg residues H6, H7, G10, Q13, A14 and G15 interact with ClfA(FIG. 1B). Remarkably, peptides g¹⁻¹⁷ _(A11S), g¹⁻¹⁷ _(D16A) and g¹⁻¹⁷_(V17A) showed an enhanced inhibition of ClfA binding to a recombinantform of residues 395-411 of the Fg g chain fused to a GST protein(GST-Fg g₁₋₁₇) compared to a peptide with the wild-type sequence,indicating a higher affinity of the peptide variants for ClfA.

The ability of ClfA₂₂₉₋₅₄₅ to bind to the peptide containing the g¹⁻¹⁷_(D16A) mutation was further characterized. In solid-phase assays, ClfAbinds to immobilized GST-Fg g¹⁻¹⁷ fusion protein with a lower affinity(K_(d)=657 nM) compared to the mutated GST-Fg g¹⁻¹⁷ _(D16A) (K_(d)=35nM) (FIG. 1C). In solution, using isothermal titration calorimetry (ITC)assays, (FIG. 1D), ClfA also binds with a lower affinity to the nativeg¹⁻¹⁷ peptide (K_(d) of 5.8 mM) compared to the mutant Fg g¹⁻¹⁷ _(D16A)(K_(d) of 3 mM). Thus, although the apparent dissociation constantsdiffer according to the assays used to estimate them, similar trends inaffinity between the wild-type and the D16A mutation were observed. Itis currently unknown why the difference between the K_(d)s was muchgreater in the solid phase binding assays compared to the ITC analysis.

The present invention demonstrates that alanine substitution at theC-terminal region of the peptide affected MSCRAMM binding suggestingthat the ClfA binding site is located at the very C-terminus of the Fgγ-chain (FIGS. 1A-1D). Results also show that certain amino acid changesin the g¹⁻¹⁷ sequence enhance ClfA binding compared to the wild-type Fgsequence indicating that the human Fg γ C-terminal 17 residues may notbe the optimum ligand for ClfA.

Analysis of the previously solved SdrG-Fg peptide complex crystalstructure showed that only 11 out of the 18 peptide residues interactedwith the MSCRAMM. Similarly, only a part of the 17-residue sequence maybe required for binding to ClfA. In order to establish the minimum Fgpeptide required for binding to ClfA₂₂₉₋₅₄₅, a series of N- andC-terminal truncations of the g¹⁻¹⁷ _(D16A) peptide were synthesized(FIG. 2A; SEQ ID NOS: 7-12 & 28). Truncations of 2, 4, 6 or 8 aminoacids at the N-terminus of the Fg g-peptide resulted in a reduced butdetectable binding affinity when tested using ITC. There was a directrelationship between the length of the peptide and its affinity forClfA. The smaller the peptide, the lower was the observed affinity forthe MSCRAMM (FIG. 2B). Thus, the N-terminal residues of the Fg peptide(residues 1-8) may either contribute to or stabilize the binding of thepeptide to ClfA, but are not critical for the interaction. On the otherhand, deletions of 2 or 4 residues from the C-terminal end of the g¹⁻¹⁷_(D16A) peptide abolished binding (data not shown). These resultsindicate that the C-terminal amino acids of Fg are critical for bindingto ClfA; these data correlate with a previous report that showed that Fglacking the C-terminal residues AGDV in the g chain (corresponding toresidues 14-17 in the peptide) or a variant that replaces the last fourg-chain residues with 20 amino acids lacks the ability to bindrecombinant ClfA₂₂₁₋₅₅₀ and or to induce S. aureus clumping (9).

Example 13 A Stabilized Closed Confirmation of ClfA₂₂₉₋₅₄₅ Binds Fg witha Higher Affinity than the Open Form

The Fg binding mechanism of SdrG₂₇₆₋₅₉₆ involves a transition from anopen conformation, where the peptide binding trench between the N2 andN3 domains is exposed for ligand docking, to a closed conformation ofthe SdrG₂₇₆₋₅₉₆ in complex with the ligand. The insertion of the N3extension into the latching trench on N2 stabilizes the closedconformation (32). The closed conformation of apo SdrG N2N3, stabilizedby introducing a disulfide bond between the end of the N3 latch and the“bottom” of N2, no longer binds Fg (32) demonstrating that the dynamicsof the latch is critical for the SdrG ligand interaction. To explore ifthe binding of ClfA to Fg is also dependent on a movement of the latch,a ClfA construct containing two cysteine substitutions was constructed.The locations of the cysteine mutations were determined using computermodeling and by sequence alignment to corresponding mutations in SdrG(32). The mutant ClfA_(D327C/K541C) generated a stable, closedconformation form. This recombinant His-tag fusion protein was purifiedby Ni⁺ chelating chromatography; ion-exchange and gel permeationchromatography. The ClfA_(D327C/K541C) open and closed conformationforms were examined by SDS-PAGE analysis (FIG. 2C).

Under non reducing conditions, the disulfide bonded closed form ofClfA_(D327C/K541C) migrated faster on SDS-PAGE than its non-disulfidebonded open form. Presumably, under non-reducing conditions, closedconformation mutants are more compact and migrate faster on SDS-PAGEthan open conformation constructs. Under reducing conditions, thedisulfide mutant and the wild-type protein migrate at the same rate.Surprisingly, the disulfide mutant ClfA_(D327C/K541C) was able to bindFg both in the open and closed conformations (FIG. 2C). Elisa-typebinding assays where Fg or GST Fg γ¹⁻¹⁷ peptide were coated inmicrotiter wells and incubated with ClfA showed that the closedconformation ClfA_(D327C/K541C) bound the ligand with a much lowerapparent K_(d) (34 nM Fg; 20 nM GST-Fg γ¹⁻¹⁷) compared to the wild-typeClfA₂₂₉₋₅₄₅ (apparent K_(d) 305 nM Fg; 222 nM GST-Fg γ¹⁻¹⁷) (FIG. 2C).These results demonstrate that an open conformation may not be requiredfor Fg binding to ClfA and that Fg binding by ClfA involves a mechanismthat is different from the DLL mechanism employed by SdrG.

Example 14 Crystal Structure of ClfA_((229-545)/D327C/K541C)) in Complexwith a 13-Residue Fg-Derived Peptide

Crystallization screens were carried out with ClfA_(D327C/K541C) incomplex with several N-terminal truncations of the g¹⁻¹⁷ _(D16A) peptidethat were shown to bind the MSCRAMM. Crystals of the stable closedconformation of ClfA₂₂₉₋₅₄₅ in complex with several peptides wereobtained, but structure determination was attempted for only theClfA_((229-545)D327C/K541C)-g⁵⁻¹⁷ _(D16A) peptide. The crystals of theClfA-peptide complex diffracted to a 1.95 Å resolution. Two copies ofClfA-peptide complex were found in the asymmetric part of the unit celland are referred to as A:C and B:D. Although the 13 residues of the Fgg⁵⁻¹⁷ chain synthetic peptide were used for crystallization, only 11residues were completely observed in both copies. The two molecules ofClfA_(D327C/K541C) (A and B) are nearly identical with rms deviation of0.3 Å for 312 Cα atoms and 0.55 Å for backbone atoms. As observed in theapo-ClfA₂₂₁₋₅₅₉ structure, the ClfA_((229-545)D327C/K541C) N2 and N3domains adopt a DE-variant IgG fold (24). The overall structure of theClfA_(D327C/K541C) peptide complex (A:C) and the two copies of thecomplexes A:C and B:D superimposed are shown in FIGS. 3A and 3B,respectively. The C-terminal extension of the N3 domain makes a β-sheetcomplementation with strand E of the N2 domain. This conformation islocked by the engineered disulfide bond as predicted by SDS-PAGEanalysis (FIG. 2C) and confirmed by the crystal structure. The twocopies of the Fg γ-peptide molecules are nearly identical with rmsdeviation of 0.5 Å for 11 Cα atoms and 0.89 Å for backbone atoms. Theinteraction between the ClfA_(D327C/K541C) and the peptide buries atotal surface area of 1849 Å² and 1826 Å² in the A:C and B:D complex,respectively. The interaction of the peptide with the N2 domain ispredominantly hydrophobic in nature, in addition to a few main-chainhydrogen bonds (FIG. 3C). Interactions between the Fg peptide and the N3domain are both hydrophobic and electrostatic with the electrostaticcontribution coming almost entirely from the main chain-main chainhydrogen bonds due to the parallel β-sheet formation of the peptide withstrand G of the N3 domain (FIG. 3C). The side-chain interactions betweenthe peptide and ClfA are predominantly hydrophobic. The 11 C-terminalresidues of the Fg g-chain peptide sequence that interact with ClfA arecomposed of only two polar residues, Lys12 and Gln13. Side chain atomsof Lys12 point away and do not interact with the ClfA protein whereasGln13 makes two hydrogen bonds with the main chain atoms of Ile 384 inClfA (FIG. 3D). A water-mediated interaction is also observed betweenGln13 of the peptide and Asn525 of ClfA. Tyr338 in the N2 domain andTrp523 in the N3 domain play an important role in anchoring the peptidemolecule. Tyr338 and Trp523 are stacked with residues Gly15 and Gly10,respectively. In addition, Met521 and Phe529 make hydrophobicinteractions with Ala7 and Val17, respectively. The C-terminal residuesof the peptide Ala14, Gly15, Ala16, and Val17 are buried between theN2-N3 domain interface with the terminal Val residue, presumablythreaded through a preformed ligand binding tunnel afterClfA_(D327C/K541C) adopted its closed conformation. A hydrogen bond isobserved between Lys389 of ClfA and the C-terminal carboxyl group of thepeptide (FIG. 6B).

Example 15 Structural Differences Between the Closed ConfirmationClfA_((D327C/541C))-Peptide Complex and the Apo-ClFA₂₂₁₋₅₅₉ Protein

The individual N2 and N3 domains in the apo-ClFA₂₂₁₋₅₅₉ and the closedform of ClfA_(D327C/K541C) are almost identical with rms deviations of0.33 and 0. Å for molecule A and 0.35 and 0.42 Å for molecule B, but therelative orientation of the N2 and N3 domains are significantlydifferent (FIG. 4A). This difference affects the association of the N2and N3 domains. In the apo conformation, the buried surface area betweenthe N2 and N3 domains is 87 Å² compared to 367 Å² in the closed form ofthe ClfA_((221-559)D327C/K541C)-peptide complex. In the apo-ClfA₂₂₁₋₅₅₉,the C-terminal residues (Ala528-Glu559) of the N3 domain fold back anddo not interact with the N2 domain.

To understand if the altered N2-N3 orientation of the apo-form of ClfA(FIG. 4A) is due to the folded-back conformation, a model of theapo-ClfA₂₂₁₋₅₅₉ was constructed with the folded-back N3 domain and theN2 domain adopting an N2-N3 orientation similar to that observed in theclosed form of the ClfA-peptide complex. This model shows that Tyr338 inthe N2 domain makes severe clashes with residues Ser535 and Gly534 ofthe folded back segment. An alternate conformation for these residues isunlikely due to spatial constraints. Thus, it is unlikely that the twodomains in the folded-back conformation could adopt an orientationsimilar to their orientation in the ClfA-peptide complex. Moreover thefolded-back segment completely occupies the binding site (FIG. 4B).Therefore, in the folded-back conformation, the ligand binding siteappear not to be accessible to the peptide.

It is presently unclear what the spatial rearrangements of the N2N3domains are in intact ClfA expressed on the surface of a staphylococcalcell. The two structures of these domains solved so far where one isactive and the other inactive provide a structural basis for thepossible regulation of ClfA's Fg binding activity by external factors.One such factor may be Ca²⁺ which has been shown to inhibit ClfA-Fgbinding (O'Connell et al., 1998). Alternatively, it is possible that thefolded-back conformation (which is a larger protein construct) is onlyone of the many possible conformations adopted by the unbound protein.Most likely, MSCRAMMs proceed from the unbound to the bound forms in avery dynamic mechanism where different intermediate forms could beachieved.

Example 16 Structural Similarities/Differences Between the Closed Formof the ClfA-Peptide and SdrG-Peptide Complexes

The major difference between Fg-binding to ClfA and SdrG is that thedirectionality of the bound ligand peptide is reversed (FIG. 4C). TheC-terminal residues of the ligand is docked between the N2 and N3 inClfA and makes a parallel β-sheet complementation with strand G of theN3 domain, whereas in SdrG, the N-terminal residues of the ligand aredocked between the N2 and N3 domains and form an anti-parallel β-sheetwith the G strand. In both cases there are 11 ligand residues that makeextensive contact with the MSCRAMM but with one residue shift towardsthe N3 domain in ClfA. Of these 11 residues, 7 and 11 residuesparticipate in the β-strand complementation of SdrG and ClfA,respectively. Although the peptide binding model of ClfA is different tothat of SdrG, the inter-domain orientations of the two MSCRAMMS are verysimilar (25). Superposition of 302 corresponding atoms in the N2 and N3domains of ClfA and SdrG showed a small rms deviation of 0.65 Åindicating the high structural similarity between the two MSCRAMMS.Another striking difference is that ClfA does not require anopen-conformation for ligand binding, whereas Fg cannot bind to astabilized closed conformation of SdrG. ClfA binds the C-terminal end ofFg and the last few residues of the γ-chain can be threaded in to thebinding pocket. In the SdrG-Fg interaction, the binding segment in Fgdoes not involve the seven N-terminal residues of the ligand andtherefore an open conformation is required for ligand binding.

Example 17 A Structural Model for Fg Binding to FnbpA

FnbpA, like ClfA, has been shown to bind the Fg γ-chain at theC-terminus. The panel of peptides with alanine substitutions (FIG. 1A)was tested as inhibitors of FnpA binding to Fg in a solid phase assay.The pattern of inhibition was similar to that measured for ClfA (FIG.7A). In addition, earlier mutational studies on FnbpA showed that tworesidues, N304 and F306, were required for full Fg binding (43). Thecorresponding residues in ClfA are P336 and Y338. Tyr 338 plays a keyrole in anchoring Gly15 of the γ-chain peptide. Together, these resultsindicate that the FnbpA Fg binding mechanism could be similar to that ofClfA. The availability of the now determined ClfA-peptide complexprompted us to model an FnbpA-Fg complex (FIG. 7B). The homology modelof the FnbpA-peptide complex showed that FnbpA can adopt a structuresimilar to that of the ClfA-ligand complex. Although there is only 25%sequence identity between ClfA and FnbpA, this model shows that almost50% of the residues that interact with the γ-chain peptide are conservedbetween FnbpA and ClfA and many others are similar. Together, thebinding data and the modeling studies suggest that ClfA and FnbpA bindFg by a similar mechanism.

Example 18 Species Variations in Fg-Binding to ClfA

There is a significant variation in the C-terminal sequences of the Fgg-chain among different animal species. The binding of ClfA_(327C/541C)to Fg isolated from different animal species was explored using asolid-phase binding assay. ClfA_(327C/541C) binds bovine Fg withsignificantly lower apparent affinity than human Fg; binding of theMSCRAMM to sheep Fg could not be detected (FIG. 5A). The bovine Fg γsequence is available and the binding data obtained in the ELISA typeassay was corroborated by measuring the affinity of ClfA_(327C/541C) forthe Fg g¹⁻¹⁷ _(D16A) peptide and a peptide representing the bovine Fg γchain sequence using ITC (FIG. 5B). A closer examination of theClfA-peptide interaction and the sequence variations between the humanand the bovine Fg γ-chain C-terminal segment suggests that two of thefour amino acid variations, at positions 14 and 16, could potentiallyexplain the difference in the affinity (FIG. 5C Upper panel). In theClfA-peptide crystal structure, Ala14 and Ala16 are completely buriedbetween the N2 and N3 domains (binding trench). Replacement of Ala withVal at either position would impose steric conflicts between ClfA andFg. However, Asp, and not Ala, is the natural sequence at position 16 ofthe peptide in human Fg. Modeling shows that Asp could adopt aconformation that could allow the side chain to point towards thesolvent with minimal steric conflict with the ClfA. The less bulky Alawould fit better in the binding site than Asp, which explains the higheraffinity of ClfA for the γ¹⁻¹⁷ _(D16A) peptide compared to the WTpeptide. Valine is branched at the Cβ atom and this residue would makesteric clashes with the residues lining the binding trench in ClfAindependent of the side-chain conformation of the Val residue. The othertwo non-contributing variations in the bovine compared to the human Fgsequence are His6→Gln and Val17→Glu. The electron density for the sidechain of His6 in the peptide is not interpretable indicating that theside-chain of the His6 and its corresponding residue, Gln, in bovine Fgdo not participate significantly in the interaction. Molecular modelingshows that even a bulkier Glu residue instead of Val at this position 17is unlikely to sterically clash with ClfA. Therefore H→Q and V→Qvariations at positions 6 and 17 may not contribute to the difference inaffinity. A specific linear sequence often appears to be recognized by astaphylococcal MSCRAMM, which raises the possibility that the MSCRAMMscan differentiate between the ligand analogs from different species.This hypothesis is illustrated herein where it can also explain instructural terms the preferential binding of ClfA to human over bovinefibrinogen. The observed species specificity of MSCRAMM ligandinteraction potentially could contribute to the observed species tropismof many staphylococcal strains.

Example 19 Comparison of Fg Binding to ClfA and the Platelet Integrinα_(IIb)β₃

The C-terminus of Fg γ-chain, which is targeted by ClfA, is alsoimportant for platelet aggregation mediated by the α_(IIb)β₃ integrin, avital step in thrombosis (9, 44). The Fg γ-chain complex with α_(IIb)β₃structure is not available but structures of related complexes provideclues on how α_(IIb)β₃ likely interact with Fg (45). In addition, thecrystal structure of the α_(v)β₃ integrin in complex with an RGD ligandprovided a structural model of a similar ligand-integrin interaction(46). In this structure, the Asp (D) residue of the RGD sequencecoordinates with the metal ion in the Metal Ion Dependent Adhesion Site(MIDAS) of the integrin and thus plays a key role in the interaction.The platelet specific integrin α_(IIb)β₃ recognizes ligands with an RGDsequence or the sequence Lys-Gln-Ala-Gly-Asp-Val (SEQ ID NO: 30) foundin Fg (45). Structural studies with drug molecules that antagonize theintegrin-RGD or -Fg interaction showed that each of the drug moleculescontains a carboxyl group moiety that mimics the aspartic acid and abasic group that mimics the Arg (or Lys in the case of Fg) in the ligand(45). These results suggest that the Lys and Asp residues in theC-terminal γ-chain sequence are critical for the interaction withintegrin. Interestingly, the present invention shows that these Lys andAsp residues in Fg are not critical for ClfA binding (FIG. 1B). In fact,substitution of Asp with Ala (γ¹⁻¹⁷ _(D16A)) results in a higher bindingaffinity. Absence of a strong interaction with Lys12 in the ClfA-peptidecomplex structure also correlates with the biochemical data, suggestingthat Arg is not a key player in the ClfA-Fg interaction. In general, thepresent invention shows that K406 and D410, which are essential forplatelet integrin α_(IIb)β₃-Fg interaction, are dispensable for theClfA-Fg interaction. Thus, although ClfA and α_(IIb)β₃ target the samestretch of amino acids in Fg, there are significant differences in thebinding interactions.

Example 20 The g¹⁻¹⁷ _(D16A) and g¹⁻¹⁷ _(K12A) Peptides are SelectiveAntagonists of Fg-ClfA Interaction

Although ClfA and α_(IIb)β₃ target the same stretch of amino acids inFg, there are significant differences in the binding interactions. Twoof the series of peptides, g¹⁻¹⁷ _(D16A) and g¹⁻¹⁷ _(K12A), synthesizedearlier for the characterization of WT g¹⁻¹⁷ peptide, lack Asp and Lysresidues respectively at positions 416 and 410. These residues arequintessential for Fg binding to plate integrin α_(IIb)β₃. The, g¹⁻¹⁷_(D16A) and g¹⁻¹⁷ _(K12A) peptides either shows similar or enhancedbinding to ClfA (FIGS. 1B, 1D) but are expected to bind weakly toplatelet integrin. Therefore, g¹⁻¹⁷ _(D16) and g¹⁻¹⁷ _(K12A) peptidescould serve as selective antagonist of Fg-ClfA interaction.

To examine this possibility, the ability of the synthesized Fg WT g¹⁻¹⁷and mutated peptides (g¹⁻¹⁷ _(D16A) and g¹⁻¹⁷ _(K12A)) to inhibit fulllength Fg binding to α_(IIb)β₃ was analyzed by inhibitory ELISA typeassay (FIG. 6). The WT, g¹⁻¹⁷ peptide completely inhibited the bindingof full-length fibrinogen to α_(IIb)β₃ whereas, g¹⁻¹⁷ _(D16A) and g¹⁻¹⁷_(K12A) weakly inhibited Fg binding α_(IIb)β₃. These results clearlydemonstrated that the g¹⁻¹⁷ _(D16A) and g¹⁻¹⁷ _(K12A) peptides bindweakly to platelet integrin and therefore could serve as an antagonistof Fg-ClfA interaction.

The following references were cited herein:

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What is claimed is:
 1. A crystal structure of a Staphylococcus clumpingfactor A protein (ClfA):fibrinogen derived peptide complex thatdiffracts x-rays for determining atomic coordinates of the complex witha resolution of at least about 2 angstroms.
 2. The crystal structure ofclaim 1, wherein the ClfA is a sequence homolog, functional homolog orboth.
 3. The crystal structure of claim 1, wherein molecularinteractions are identified for ClfA residues 521-529 and fibrinogen. 4.The crystal structure of claim 1, wherein residues 522, 524, 526 and 528are involved in mainchain-mainchain hydrogen bonding interaction; sidechain of Trp523 is involved in anchoring the gamma chain of fibrinogen;side chain of Asn525 is involved in hydrogen bonding interaction withGln408 of fibrinogen; residue 521 has hydrophobic interaction with gammachain of fibrinogen; residue 526 does not have any side chaininteraction with fibrinogen and may not be a key residue in fibrinogenbinding; residue 528 does not have any side chain interaction withfibrinogen and may not be a key residue in fibrinogen gamma chainbinding; or residue 529 has hydrophobic interaction with glycine residue409 in the gamma chain of fibrinogen.
 5. A therapeutic agent comprisinga binding agent that (1) disrupts interaction at residues 521 to 529 ofa clumping factor A protein (ClfA) with a gamma chain of a fibrinogen;(2) disrupts interaction at residues 505-513 in Fbl with a gamma chainof a fibrinogen; or (3) disrupts interaction at residues 492-500 inFnbpA with a gamma chain of a fibrinogen, wherein the binding agent is amonoclonal antibody, small molecule, or peptide
 6. A therapeutic agentthat blocks the interaction of microbial surface components recognizingadhesive matrix molecules (MSCRAMMs) with fibrinogen comprising: atherapeutic agent with at least 85% homology to residues 521-529 ofClfA; residues 492-500 of Fbl; residues 505-513 of FnbpA or acombination thereof, wherein the therapeutic agent reduces MSCRAMMsinteractions with a gamma chain of a fibrinogen
 7. The therapeutic agentof claim 6, wherein the residues 521-529 of ClfA are involved in eithermainchain-mainchain interaction or interactions involving side chains.8. The therapeutic agent of claim 6, wherein the therapeutic agentsupports both a fibrinogen gamma chain binding and maintains astructural fold by maintaining a B-sheet with a N3 domain.
 9. Thetherapeutic agent of claim 6, wherein the therapeutic agent has at least85% homology to residues 521-529 of ClfA and residues 522, 524, 526 and528 are involved in mainchain-mainchain hydrogen bonding interaction.10. The therapeutic agent of claim 6, wherein the therapeutic agent hasat least 85% homology to residues 521-529 of ClfA and a side chain ofTrp523 is involved in anchoring the gamma chain of fibrinogen.
 11. Thetherapeutic agent of claim 6, wherein the therapeutic agent has at least85% homology to residues 521-529 of ClfA and a side chain of Asn525 isinvolved in hydrogen bonding interaction with Gln408 of fibrinogen. 12.The therapeutic agent of claim 6, wherein the therapeutic agent has atleast 85% homology to residues 521-529 of ClfA and residue 521 hashydrophobic interaction with a gamma chain of a fibrinogen.
 13. Thetherapeutic agent of claim 6, wherein the therapeutic agent has at least85% homology to residues 521-529 of ClfA and residue 526 does not haveany side chain interaction with a fibrinogen and may not be a keyresidue in fibrinogen binding.
 14. The therapeutic agent of claim 6,wherein the therapeutic agent has at least 85% homology to residues521-529 of ClfA and residue 528 does not have any side chain interactionwith fibrinogen and may not be a key residue in fibrinogen gamma chainbinding.
 15. The therapeutic agent of claim 6, wherein the therapeuticagent has at least 85% homology to residues 521-529 of ClfA and residue529 has a hydrophobic interaction with a glycine residue 409 in a gammachain of a fibrinogen.
 16. The therapeutic agent of claim 6, wherein thetherapeutic agent has at least 85% homology to residues 521-529 of ClfAand further comprises a hydrophobic interactions with an alanine residue401 in a gamma chain of a fibrinogen.
 17. The therapeutic agent of claim6, wherein the therapeutic agent is homologous to MSWDNEVAF, MAWDNEVEY,or LTWDNGLVLY.
 18. A method of identifying and targeting gamma chainbinding MSCRAMMs/bacterial proteins comprising the steps of: providing acrystal structure of a clumping factor A protein (ClfA):fibrinogenderived peptide complex; providing a targeting sequence to identify thefibrinogen gamma chain binding target.
 19. The method of claim 18,wherein the targeting sequence is homologous to residues 521-529 ofClfA.
 20. The method of claim 18, wherein the targeting sequence ishomologous to residues 492-500 of Fbl.
 21. The method of claim 18,wherein the targeting sequence is homologous to residues 505-513 ofFnbpA.
 22. The method of claim 18, wherein the targeting sequence ishomologous to MSWDNEVAF, MAWDNEVEY, or LTWDNGLVLY.